Grain-free chocolate cupcakes (Primal, GAPS, Grain-Free, Gluten-Free)

What to do when your grain-free recipes don’t “hold a candle” to the old stand-by recipes for cupcakes, cookies, and cakes? It can take a lot of trial and error to adapt recipes to a gut-healing diet, and still taste good. In this post, I will describe how to make grain-free chocolate cupcakes that are just as delicious as the sugary, gluten-full versions.

I am happy to say that this cupcake recipe holds up.

We’ve made these cupcakes for countless birthdays, potlucks where there were gluten-free eaters, and other special occasions.

Important note: Cocoa and baking soda are allowed on the GAPS Diet, but only when all digestive symptoms are gone, and only on the Full GAPS Diet.

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Grain-Free Chocolate Cupcakes (Primal, GAPS, Grain-free, Gluten-free)

5 Stars 4 Stars 3 Stars 2 Stars 1 Star 4.9 from 14 reviews
  • Author: Melanie Christner - Honest Body


Makes 12+ cupcakes

Adapted from this recipe by Comfy Belly


  • 1/2 cup coconut flour
  • 1/2 cup unsweetened cocoa (fair trade best)
  • 1/2 tsp unrefined sea salt
  • 1/2 tsp baking soda
  • 6 large eggs
  • 1 cup raw honey
  • 1/4 cup (1/2 stick) butter


  1. Preheat oven to 350 degrees F
  2. Combine all the dry ingredients and mix well
  3. Melt butter in saucepan over low heat
  4. Mix eggs, honey and melted butter together
  5. Combine wet ingredients with dry ingredients and mix for at least a minute or more, until smooth without clumps (coconut flour expands as it takes in moisture, so it is good to give it a little time)
  6. Fill each cupcake liner 1/2 way up
  7. Bake for about 20 minutes, or until a toothpick inserted comes out clean.
  8. Cool cupcakes before applying frosting
  9. Frost and enjoy! You can store these at room temp or in the fridge. The buttercream frosting will stay “in shape” better in the fridge.

Chocolate Buttercream Frosting

  • 2 sticks, or 1 cup butter (softened to room temp)
  • 2/3 cup honey
  • 4 Tbs unsweetened cocoa


  • Combine in mixer and blend until smooth and pliable enough to go into a pastry bag for piping

Try these out for your next birthday party or family celebration…they will be a hit!

This simple grain-free chocolate cupcake recipe will be your go-to recipe the first time you try them! Perfect for GAPS and grain or gluten-free diets.


71 thoughts on “How To Make Grain-Free Chocolate Cupcakes (Primal, GAPS, Grain-free, Gluten-free)”

    1. Melanie Christner

      Hi Anna,

      Thanks for the question. You can sub maple syrup, but I find that I don’t like the texture/taste quite as much…and if you are on the GAPS™ protocol, you’ll need to avoid maple syrup.

  1. OMG… I cannot believe how amazingly great these are! my 11 year old has NO idea they are not regular cupcakes- that is very hard to do! thank you SO much

    1. Melanie Christner

      Hi Tammy,

      Thanks for the question. The frosting in the picture is the chocolate buttercream frosting that is below the cupcake recipe in the post. Enjoy 🙂

        1. Melanie Christner

          Hi Gina,

          Each stick of butter is equal to = 8 tablespoons, or 1/2 cup, or 113 grams, or 4 ounces. Thanks for the question!


  2. Um, yeah. I’ve kind of accepted that GAPS desserts aren’t ever going to be as tasty as other desserts…until today. THANK YOU MELANIE!

    1. Melanie Christner

      Hi Paola,

      Thank you for commenting. I’m so glad you liked our blueberry cream cheese dessert!


  3. Hi! These look wonderful and I am very excited to try them. Would coconut oil work as a sub for butter? Also, do you think these would freeze ok? Thanks!

  4. Hello Melanie! I stumbled across your beautiful blog when trying to find a chocolate cake recipe with coconut flour I could make with the ingredients on hand. I sure am glad I decided to try this instead of the sheet cake my heart was after. These are so delicious they almost bring tears of joy! I love your design and layout, but besides all that, I LOVE this recipe. I’m honestly amazed that such simple ingredients come together and taste this amazing. At first I was quite worried because the batter was far more liquid than normal, but I followed the recipe and the result was absolutely amazing! Mine yielded 18 cupcakes. I skipped the frosting out of laziness, and that is OK with me because they are so rich and sweet just the way they are! I used MyFitnessPal to count the nutrition information for each cup cake and this is what I came up with: Calories 122, Fat(g) 5, Saturated(g) 2.8, Polyunsaturated(g) 0.1, Monounsaturated(g) 0.8, Trans(g) 0, Cholesterol(mg) 68.4, Sodium(mg) 132.1, Potassium(mg) 47, Carbs(g) 18.6, Fiber(g) 1.9, Vitamin A(%) 3.6, Vitamin C(%) 0.2, Calcuim(%) 1.2, Iron(%) 5.8. I am in love with this recipe! Thank you so much! I’ve shared your blog on my Facebook page and my MyFitnessPal page because I love it so much. Keep the recipes coming and happy baking!

    1. Melanie Christner

      Hi Shelsea,

      I’m so glad you enjoyed the chocolate cupcake recipe! It’s one of our family favorites as well.

      Thank you,

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    1. Melanie Christner

      Hi Sarah,

      A stick of butter is equal to: 1/4 lb., 1/2 cup, and 113.39 grams.

      Thanks for your question,

  7. Hi, you said, “Mix eggs, honey and melted honey together”

    I assume you meant to say, “Mix eggs, honey and melted butter together”?

    1. Melanie Christner

      Hi Darla,

      This works very well for cakes, yes. You’ll just need to adjust to a longer baking period.


  8. Melanie!!!!! (Hi! We miss you guys a ton!) These cupcakes are amazing and I’m sold! These will be my go-to from now on. I added the strawberry buttercream on top and that was equally as awesome. You rock! Thanks!

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    1. Melanie Christner

      Hi Carol,

      If you live somewhere where it is quite warm, I would recommend it, as the buttercream frosting would get too soft. Otherwise they should be fine for one day unrefrigerated.


      1. Thanks for the quick response. I see now that you mention refrigerating them in the recipe. Just took them out of the oven and I have a feeling they will taste as good as they look. Can’t wait to try one! Thanks again!

    1. Melanie Christner

      Hi Dee,

      Thanks for your question. These are our favorite cupcakes…the feedback I get is that you can’t even tell they are grain-free.

      Let me know what you think though, if you try them 🙂


  11. This recipe could rescue my sanity. The reviews are encouraging, my only concern is the use of honey. I don’t like the taste of honey and I was wondering if the taste is noticeable in the cupcakes. If it is, do you think I could use coconut sugar without changing the results of finished product? Or maybe use date preserves instead?

    1. Melanie Christner

      Hi Raquel,

      Thanks for your question. I think that the chocolate flavor lends itself nicely to masking the honey flavor. I haven’t tried making this particular recipe with coconut sugar but if you do, let us know how it turns out…you may need to adjust a little for the lack of honey moistness?


  12. Hi this is a awesome cupcake. I love them! I am making them for my friends b day party. I am sure they will love them to! 🙂

  13. I know I’m late to the party, but I have a few questions:

    My understanding is Ghee can be substituted for the butter just the same. Is that correct?
    And for one with a food allergy to dairy, would Ghee be an acceptable substitute, or should I simply start out with Coconut Oil and not risk it to start?

    And, could one substitute Carbo Powder for the Cocoa Powder?

    I have a friend with severe allergies to Gluten, Dairy, and even Caffeine. Trying to find something resembling a chocolate dessert, being a recovering chocoholic myself, that she can also enjoy at an upcoming party.

    1. Melanie Christner

      Hi Timothy,

      Thanks for the questions 🙂

      Ghee can be substituted for butter, but I would hesitate to do this for someone with a true allergy to dairy. I would use coconut oil for your friend. It won’t quite have the same “buttery” taste but will be good nonetheless.

      I’m sorry I can’t speak for the carob powder substitution as I haven’t tried it in this recipe…experiment at home?

      Melanie 🙂

  14. Hello there,

    I’ve made these and loved them for my son’s birthday. This year he wants a cake, will this recipe work? If so, what size pan and cooked how long? If not, do you have one similar that works for cake?? Thanks!

    1. Melanie Christner

      Hi Janie,

      This recipe works for cake as well, yes. I would suggest doubling the recipe and using 2 “regular” size 9″ round cake pans. You can bake at the same temperature, but slightly longer.

  15. Melissa Patterson

    Hi. My daughter’s birthday is this weekend and she wants a chocolate cupcake with vanilla frosting. These look and sound amazing. Can I make the frosting vanilla by taking out the chocolate and adding vanilla, coconut butter, or something? Many thanks! Melissa

  16. I used this recipe as a cake and everyone, including my family members with major sweet tooth and no food allergies, LOVED it! I am baking again as cupcakes for my son’s bday this weekend. So far this is his favorite recipe! Thank you!!!

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    1. Melanie Christner

      Hi Jinny,

      I know it is proper to use unsalted butter for baking, but I tend to use lightly salted butter because it is on hand. 🙂


  18. I love this recipe and used it last on my gaps son’s birthday. Today, I am trying it with coffee flour recommended by my son’s doctor after he is not tolerating nuts and coconut flour. We can hope to get the same good results!

    1. By the way it is hard to get this batter to the cupcake tins for cooking because my son wants to eat it right out of the mixing bowl. I also add a half tsp cinnamon for flavor.

    1. Melanie Christner

      Hello Stephanie,

      I have not, but great question…if you do try it, let us know how it turned out?


  19. My son is allergic to coconut- can you substitute almond flour for the coconut flour? And if so, how much would be equivalent for this recipe? He has so many allergies and special diets- I am very excited to try this recipe for his upcoming birthday!

  20. My friend made these recently, delicious and fluffy! I wwould love to try it for my son but he doesn’t like chocolate. Any way that removing the chocolate and/or substituting it for something else would work? He really only likes vanilla flavour (ie white) or carrot cakes. If you have other such cakes I’ve missed I’d love to give it a try. Thanks a million!

  21. Oh my goodness! These are amazing!!! I keep thinking I will try your strawberry cupcakes one of these days, but I keep making these instead. Thank you! ?

  22. Made this recipe today after the local cupcake store was out of GF cupcakes. I replaced the cocoa powder with cricket protein powder and reduced the amount of honey by almost 1/3. Also whipped the egg whites first and then folded them into the batter for a super light and fluffy cupcake. Same with the buttercream – no cocoa and substituted it for cricket protein powder and only used 1/3 c honey. Beat until the cream was light and fluffy. This is one awesome cupcake base recipe! Very versatile.

    1. Melanie Christner

      Hello Pollete,

      Butter is allowed on GAPS once you have gone through the dairy introduction schedule.


  23. These cupcakes were amazing! So moist and fluffy. My kids loved them as well! The only thing is my cupcakes didn’t rise like the way your look in your picture..I did add chocolate chips to mine ..I wonder if that’s why?

  24. I have a daughter who has eczema and asthma. There are many food that she can’t eat. I used this recipe for her birthday. She enjoyed it. Thanks for the recipe!

    1. Melanie Christner

      Hi Grace,

      Thank you for the feedback! I’m glad your daughter was able to enjoy this recipe on her birthday 🙂


  25. Annelle Prefontaine

    I need to replace the eggs with egg substitute . Have you gotten any comments From Stephanie. She asked the same question. On how hers came out with egg replacer?? Thanks in advance for your help.

    1. Hi Annelle,
      Thanks for checking in on that. I have not seen anything specific from Stephanie on how the egg replacement worked. Here’s a pretty thorough article on egg replacement with a specific comment regarding coconut flour: that might help. If you end up trying the recipe with an egg replacer please let us know how it turned out!

      Deanna, Honest Body Assistant and Certified GAPS Coach

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